The invention relates in general to the reproducible, mass-production of nucleic acid arrays. The invention also relates to methods of sequencing nucleic acids on arrays.
Arrays of nucleic acid molecules are of enormous utility in facilitating methods aimed at genomic characterization (such as polymorphism analysis and high-throughput sequencing techniques), screening of clinical patients or entire pedigrees for the risk of genetic disease, elucidation of protein/DNA- or protein/protein interactions or the assay of candidate pharmaceutical compounds for efficacy; however, such arrays are both labor-intensive and costly to produce by conventional methods. Highly ordered arrays of nucleic acid fragments are known in the art (Fodor et al., U.S. Pat. No. 5,510,270; Lockhart et al., U.S. Pat. No. 5,556,752). Chetverin and Kramer (WO 93/17126) are said to disclose a highly ordered array which may be amplified.
U.S. Pat. No. 5,616,478 of Chetverin and Chetverina reportedly claims methods of nucleic acid amplification, in which pools of nucleic acid molecules are positioned on a support matrix to which they are not covalently linked. Utermohlen (U.S. Pat. No. 5,437,976) is said to disclose nucleic acid molecules randomly immobilized on a reusable matrix.
There is need in the art for improved methods of nucleic acid array design and production. There is also a need in the art for methods with improved resolution and/or sensitivity for detection of sequences on nucleic acid arrays. There is also a need in the art for improved methods of sequencing the molecules on nucleic acid arrays.
The invention provides a method of producing a high density array of immobilized nucleic acid molecules, such method comprising the steps of: 1) creating an array of spots of a nucleic acid capture activity such that the spots of said capture activity are separated by a distance greater than the diameter of the spots, and the size of the spots is less than the diameter of the excluded volume of the nucleic acid molecule to be captured; 2) contacting the array of spots of nucleic acid capture activity with an excess of nucleic acid molecules with an excluded volume diameter greater than the diameter of the spots of nucleic acid capture activity, resulting in an immobilized array of nucleic acid molecules in which each spot of nucleic acid capture activity can bind only one nucleic acid molecule with an excluded volume diameter greater than the size of said spots of nucleic acid capture activity.
In a preferred embodiment of the invention, the nucleic acid capture activity may be a hydrophobic compound, an oligonucleotide, an antibody or fragment of an antibody, a protein, a peptide, an intercalator, biotin, avidin, or streptavidin.
In another embodiment of the invention the immobilized array of spots of a nucleic acid capture activity are arranged in a predetermined geometry.
In another embodiment, the immobilized spots of a nucleic acid capture activity are aligned with other microfabricated features.
The invention also encompasses a method of making a plurality of a high-density nucleic acid array made using spots of nucleic acid capture activity as described above.
The invention provides a method for the detection of a nucleic acid on an array of nucleic acid molecules, such method comprising the steps of generating a plurality of a nucleic acid molecule array wherein the nucleic acid molecules of each member of said plurality occupy positions which correspond to those positions occupied by the nucleic acid molecules of each other member of said plurality of a nucleic acid array, and subjecting one or more members of said plurality, but at least one less than the total number of said plurality to a method of signal detection comprising a signal amplification method which renders said member of said plurality of a nucleic acid array non-reusable.
It is preferred that the signal amplification method comprises fluorescence measurement.
In a preferred embodiment the method of detection of a nucleic acid on an array of nucleic acid molecules detects the amount of an RNA expressed in a first RNA-containing nucleic acid population relative to that expressed in a second RNA-containing nucleic acid population. The method further comprises the steps of preparing a first population of fluorescently labeled cDNA using said first population of RNA containing nucleic acid as a template, preparing a second fluorescently labeled cDNA population using said second population of RNA-containing nucleic acid as a template, said second fluorescently labeled cDNA population being labeled with a fluorescent label distinguishable from that used to label said first population, contacting a mixture of said first fluorescently labeled cDNA population and said second fluorescently labeled cDNA population with a member of said plurality of nucleic acid arrays under conditions which permit hybridization of said fluorescently labeled cDNA populations with nucleic acids immobilized on said members of said plurality of nucleic acid arrays and detecting the fluorescence of said first fluorescently labeled population of cDNA and the fluorescence of said second fluorescently labeled population of cDNA hybridized to said member of said plurality of nucleic acid arrays, wherein the relative amount of said first fluorescent label and said second fluorescent label detected on a given nucleic acid feature of said array indicates the relative level of expression of RNA derived from the nucleic acid of that feature in the mRNA-containing cDNA populations tested.
In another embodiment the method of detection of a nucleic acid on an array of nucleic acid molecules detects the amount of an RNA expressed in a first RNA-containing nucleic acid population relative to that expressed in a second RNA-containing nucleic acid population. The method further comprises the steps of preparing a first population of fluorescently labeled cDNA using said first population of RNA containing nucleic acid as a template, preparing a second fluorescently labeled cDNA population using said second population of RNA-containing nucleic acid as a template, contacting said first fluorescently labeled cDNA population with one member of a plurality of immobilized nucleic acid arrays under conditions which permit hybridization of said fluorescently labeled cDNA population with nucleic acid immobilized on said member of a plurality of immobilized nucleic acid arrays, contacting said second fluorescently labeled cDNA population with another member of the same plurality of immobilized nucleic acid arrays under conditions which permit hybridization of said fluorescently labeled cDNA populations with nucleic acid immobilized on said members of a plurality of immobilized nucleic acid arrays, detecting the intensity of fluorescence on each member of said plurality contacted with a fluorescently labeled cDNA population, and comparing the intensity of fluorescence detected on each member of said plurality of immobilized nucleic acid arrays so tested, to determine the relative expression of mRNA derived from those nucleic acids on the array in the mRNA-containing cDNA populations tested.
The invention provides a method of preserving the resolution of nucleic acid features on a first immobilized array during cycles of array replication, said method comprising the steps of: a) amplifying the features of a first array to yield an array of features with a hemispheric radius, r, and a cross-sectional area, q, at the surface supporting said array, such that said features remain essentially distinct; b) contacting said array of features with a radius, r, with a support, maintained at a fixed distance from said first array, said fixed distance less than r, and such that the cross-sectional area of the hemispheric feature, measured at said fixed distance from the surface supporting said first array is less than q, and such that at least a subset of nucleic acid molecules produced by said amplifying are transferred to said support; c) covalently affixing said nucleic acid molecules to said support to form a replica of said first immobilized array, wherein the positions of said nucleic acid molecules on said replica correspond to the positions of said nucleic acid molecules of said first array from which they were amplified, and wherein the areas occupied on the surface of said support by the individual features of said replica are less than the areas occupied on the surface supporting said first immobilized array.
It is preferred that said amplifying be performed by PCR.
In another embodiment of the method of preserving the resolution of nucleic acid features on a first immobilized array during cycles of array replication, the method is repeated to yield further replicas with preserved resolution.
The invention provides a method for determining the nucleotide sequence of the features of an immobilized nucleic acid array, such method comprising the steps of: a) ligating a first double-stranded nucleic acid probe to one end of a nucleic acid of a feature of said array, said first double stranded nucleic acid probe having a restriction endonuclease recognition site for a restriction endonuclease whose cleavage site is separate from its recognition site and which generates a protruding strand upon cleavage; b) identifying one or more nucleotides at the end of said polynucleotide by the identity of the first double stranded nucleic acid probe ligated thereto or by extending a strand of the polynucleotide or probe; c) amplifying the features of said array using a primer complementary to said first double stranded nucleic acid probe, such that only molecules which have been successfully ligated with said first double stranded nucleic acid probe are amplified to yield an amplified array; d) contacting said amplified array with support such that at least a subset of nucleic acid molecules produced by said amplifying are transferred to said support; e) covalently attaching said subset of nucleic acid molecules to said support to form a replica of said amplified array; f) cleaving the nucleic acid features of the array with a nuclease recognizing said nuclease recognition site of said probe such that the nucleic acid of the features is shortened by one or more nucleotides; and g) repeating steps (a)-(f) until the nucleotide sequences of the features of said array are determined.
It is preferred that the nucleic acid probe comprises four components, each component being capable of indicating the presence of a different nucleotide in the protruding strand upon ligation. It is further preferred that each of the components of the probe is labeled with a different fluorescent dye and that the different fluorescent dyes are spectrally resolvable.
In another embodiment of the invention, the features of the array are amplified after step (e) and before step (f).
It is preferred that the amplifying be accomplished by PCR.
In another embodiment, the method of determining the sequence of the features of an immobilized nucleic acid array is modified such that: i) after one or more cycles using said first double stranded nucleic acid probe in step (a), a distinct nucleic acid probe is used, in place of said first double stranded nucleic probe, said distinct nucleic acid probe comprising a restriction endonuclease recognition site for a restriction endonuclease whose cleavage site is separated from its recognition site, said distinct nucleic acid probe also comprising sequences such that a primer complementary to said distinct nucleic acid probe will not hybridize with said first double stranded nucleic acid probe; and ii) a primer complementary to said distinct nucleic acid probe is used in place of said primer complementary to said first double stranded nucleic acid probe in step (c), so that selective amplification of those features which successfully completed the previous cycle of restriction and ligation occurs.
In another embodiment of this modified method of determining the nucleotide sequence of the features of an immobilized nucleic acid array, a new distinct nucleic acid probe is used after each cycle of restriction and ligation, said new distinct nucleic acid probe comprising a sequence such that a primer complementary to that sequence will not hybridize to any probe used in previous cycles.
The invention provides a method of determining the nucleotide sequence of the features of an array of immobilized nucleic acids comprising the steps of: a) adding a mixture comprising an oligonucleotide primer and a template-dependent polymerase to an array of immobilized nucleic acid features under conditions permitting hybridization of the primer to the immobilized nucleic acids; b) adding a single, fluorescently labeled deoxynucleoside triphosphate to the mixture under conditions which permit incorporation of the labeled deoxynucleotide onto the 3xe2x80x2 end of the primer if it is complementary to the next adjacent base in the sequence to be determined; c) detecting incorporated label by monitoring fluorescence; d) repeating steps (b)-(c) with each of the remaining three labeled deoxynucleoside triphosphates in turn; and e) repeating steps (b)-(d) until the nucleotide sequence is determined.
In a preferred embodiment, the primer, buffer and polymerase are cast into a polyacrylamide gel bearing the array of immobilized nucleic acids.
It is preferred that the single fluorescently labeled deoxynucleotide further comprises a mixture of the single deoxynucleoside triphosphate in labeled and unlabeled forms.
In another embodiment, the additional step of photobleaching said array is performed after step (d) and before step (e).
In another embodiment, the fluorescently labeled deoxynucleoside triphosphates are labeled with a cleavable linkage to the fluorophore, and the additional step of cleaving said linkage to the fluorophore is performed after step (d) and before step (e).
In another embodiment, the oligonucleotide primer comprises sequences permitting formation of a hairpin loop.
In another embodiment, after a predetermined number of cycles of steps (b)-(d), a defined regimen of deoxynucleotide and chain-terminating deoxynucleotide analog addition is performed, such that out-of-phase molecules are blocked from further extension cycles, said regimen followed by continued cycles of steps (b)-(d) until the nucleotide sequence of the features of the array is determined.
The invention provides a method of determining the nucleotide sequence of the features of an array of immobilized nucleic acids comprising the steps of: a) adding a mixture comprising an oligonucleotide primer and a template-dependent polymerase to an array of immobilized nucleic acid features under conditions permitting hybridization of the primer to the immobilized nucleic acids; b) adding a first mixture of three unlabeled deoxynucleoside triphosphates under conditions which permit incorporation of deoxynucleotides to the end of the primer if they are complementary to the next adjacent base in the sequence to be determined; c) adding a second mixture of three unlabeled deoxynucleoside triphosphates, along with buffer and polymerase if necessary, said second mixture comprising the deoxynucleoside triphosphate not included in the mixture of step (b), under conditions which permit incorporation of deoxynucleotides to the end of the primer if they are complementary to the next adjacent base in the sequence to be determined; d) repeating steps (b)-(c) for a predetermined number of cycles; e) adding a single, fluorescently labeled deoxynucleoside triphosphate to the mixture under conditions which permit incorporation of the labeled deoxynucleotide onto the 3xe2x80x2 terminus of the primer if it is complementary to the next adjacent base in the sequence to be determined; f) detecting incorporated label by monitoring fluorescence; g) repeating steps (e)-(f), with each of the remaining three labeled deoxynucleoside triphosphates in turn; and h) repeating steps (e)-(g) until the nucleotide sequence is determined.
It is preferred that for the first or second mixtures of three unlabeled deoxynucleoside triphosphates, a mixture which comprises deoxyguanosine triphosphate further comprises deoxyadenosine triphosphate.
In a preferred embodiment, method the primer and polymerase are cast into a polyacrylamide gel bearing the array of immobilized nucleic acids.
In a preferred embodiment, the single fluorescently labeled deoxynucleotide further comprises a mixture of the single deoxynucleoside triphosphate in labeled and unlabeled forms.
In another embodiment of this method of determining the nucleotide sequence of nucleic acid features on an array, the additional step of photobleaching the array is performed after step (g) and before step (h).
In another embodiment of this method of determining the nucleotide sequence of nucleic acid features on an array, the fluorescently labeled deoxynucleoside triphosphates are labeled with a cleavable linkage to the fluorophore and after step (g) and before step (h) the additional step of cleaving the linkage to the fluorophore is performed.
In another embodiment of this method of determining the nucleotide sequence of nucleic acid features on an array, the oligonucleotide primer comprises sequences permitting formation of a hairpin loop.
In another embodiment of this method of determining the nucleotide sequence of nucleic acid features on an array, after a predetermined number of cycles of steps (e)-(g), a defined regimen of deoxynucleotide and chain-terminating deoxynucleotide analog addition is performed, such that out-of-phase molecules are blocked from further extension cycles, said regimen followed by continued cycles of steps (e)-(g) until said nucleotide sequence is determined.
The invention provides a method of determining the nucleotide sequence of the features of a micro-array of nucleic acid molecules, said method comprising the steps of: a) creating a micro-array of nucleic acid features in a linear arrangement within and along one side of a polyacrylamide gel, said gel further comprising one or more oligonucleotide primers, and a template-dependent polymerizing activity; b) amplifying the microarray; c) adding a mixture of deoxynucleoside triphosphates, said mixture comprising each of the four deoxynucleoside triphosphates DATP, dGTP, dCTP and dTTP, said mixture further comprising chain-terminating analogs of each of the deoxynucleoside triphosphates dATP, dGTP, dCTP and dTTP, and said chain-terminating analogs each distinguishably labeled with a spectrally distinguishable fluorescent moiety; d) incubating said mixture with said micro-array under conditions permitting extension of said one or more oligonucleotide primers; e) electrophoretically separating the products of said extension within said polyacrylamide gel; and f) determining the nucleotide sequence of the features of said micro-array by detecting the fluorescence of the extended, terminated and separated reaction products within the gel.
It is preferred that the amplifying be performed by PCR.
In another embodiment, the amplifying may be performed by an isothermal method.
In another embodiment the microarray of nucleic acid features in a linear arrangement is derived as a replica of features arranged on a chromosome.
In another embodiment the microarray of nucleic acid features in a linear arrangement is derived as a replica of one linear subset of features on a separate, non-linear micro-array of nucleic acid features.
The invention provides a method of simultaneously amplifying a plurality of nucleic acids, said method comprising the steps of: a) creating a micro-array of immobilized oligonucleotide primers; b) incubating the microarray with amplification template and a non-immobilized oligonucleotide primer under conditions allowing hybridization of said template with said oligonucleotide primers; c) incubating the hybridized primers and template with a DNA polymerase activity, and deoxynucleotide triphosphates under conditions permitting extension of the primers; d) repeating steps (b) and (c) for a defined number of cycles to yield a plurality of amplified DNA molecules.
It is preferred that the non-immobilized oligonucleotide primer comprises a pool of oligonucleotide primers comprised of 5xe2x80x2 and 3xe2x80x2 sequence elements, said 5xe2x80x2 sequence element identical in all members of said pool, and said 3xe2x80x2 sequence element containing random sequences.
It is preferred that the 5xe2x80x2 sequence element comprises a restriction endonuclease recognition sequence.
In another embodiment, the 5xe2x80x2 sequence element comprises a transcriptional promoter sequence.
In another embodiment, the immobilized primers are amplified before step (b).
In another embodiment, the immobilized oligonucleotide primers are generated from genomic DNA.
In a preferred embodiment, the microarray, template, non-immobilized primer, and polymerase are cast in a polyacrylamide gel.
The invention provides a method of making an immobilized nucleic acid molecule array, the method comprising: a) providing template DNA and a pair of PCR primers, wherein at least one member of the pair is Acrydite modified; b) mixing the template DNA and PCR primers with a solution comprising acrylamide monomers; c) contacting the mixture of step (b) with a solid support and polymerizing the acrylamide monomers; and d) amplifying the template DNA by PCR to generate an immobilized nucleic acid molecule array.
In a preferred embodiment, the solid support is a glass microscope slide.
In another preferred embodiment, the solution comprising acrylamide monomers further comprises a template-dependent DNA polymerase.
In another preferred embodiment, the polymerase is Taq DNA polymerase.
In another preferred embodiment, the template DNA comprises binding sites for the pair of PCR primers, with one binding site on each side of a variable sequence.
In another preferred embodiment, the template DNA comprises a library.
The invention provides a method of making a plurality of an immobilized nucleic acid molecule array, the method comprising: a) providing template DNA and a pair of PCR primers, wherein at least one member of the pair of PCR primers is Acrydite modified; b) mixing the template DNA and pair of PCR primers with a solution comprising acrylamide monomers; c) contacting the mixture of step (b) with a solid support that binds to polyacrylamide, and polymerizing the acrylamide monomers to form a first layer; d) contacting the first layer with a mixture comprising the pair of PCR primers and acrylamide monomers, and polymerizing the acrylamide monomers to form a second layer; e) amplifying the template DNA by PCR to generate an immobilized nucleic acid molecule array; f) removing the second layer, wherein the second layer comprises a duplicate of the array; and g) repeating steps d-f one or more times to generate a plurality of an immobilized nucleic acid molecule array.
In a preferred embodiment, the solid support is a glass microscope slide.
In another preferred embodiment, the solution comprising acrylamide monomers further comprises a thermostable, template-dependent DNA polymerase.
In another preferred embodiment, the polymerase is Taq DNA polymerase.
In another preferred embodiment, the template DNA comprises binding sites for the pair of PCR primers, with one binding site on each side of a variable sequence.
In another preferred embodiment, the template DNA comprises a library.
As used herein in reference to nucleic acid arrays, the term xe2x80x9cpluralityxe2x80x9d is defined as designating two or more such arrays, wherein a first (or xe2x80x9ctemplatexe2x80x9d) array plus a second array made from it comprise a plurality. When such a plurality comprises more than two arrays, arrays beyond the second array may be produced using either the first array or any copy of it as a template.
As used herein, the terms xe2x80x9crandomly-patternedxe2x80x9d or xe2x80x9crandomxe2x80x9d refer to a non-ordered, non-Cartesian distribution (in other words, not arranged at pre-determined points along the x- and y axes of a grid or at defined xe2x80x98clock positionsxe2x80x99, degrees or radii from the center of a radial pattern) of nucleic acid molecules over a support, that is not achieved through an intentional design (or program by which such a design may be achieved) or by placement of individual nucleic acid features. Such a xe2x80x9crandomly-patternedxe2x80x9d or xe2x80x9crandomxe2x80x9d array of nucleic acids may be achieved by dropping, spraying, plating or spreading a solution, emulsion, aerosol, vapor or dry preparation comprising a pool of nucleic acid molecules onto a support and allowing the nucleic acid molecules to settle onto the support without intervention in any manner to direct them to specific sites thereon.
As used herein, the terms xe2x80x9cimmobilizedxe2x80x9d or xe2x80x9caffixedxe2x80x9d refer to covalent linkage between a nucleic acid molecule and a support matrix.
As used herein, the term xe2x80x9carrayxe2x80x9d refers to a heterogeneous pool of nucleic acid molecules that is distributed over a support matrix; preferably, these molecules differing in sequence are spaced at a distance from one another sufficient to permit the identification of discrete features of the array.
As used herein, the term xe2x80x9cheterogeneousxe2x80x9d is defined to refer to a population or collection of nucleic acid molecules that comprises a plurality of different sequences; it is contemplated that a heterogeneous pool of nucleic acid molecules results from a preparation of RNA or DNA from a cell which may be unfractionated or partially-fractionated.
An xe2x80x9cunfractionatedxe2x80x9d nucleic acid preparation is defined as that which has not undergone the selective removal of any sequences present in the complement of RNA or DNA, as the case may be, of the biological sample from which it was prepared. A nucleic acid preparation in which the average molecular weight has been lowered by cleaving the component nucleic acid molecules, but which still retains all sequences, is still xe2x80x9cunfractionatedxe2x80x9d according to this definition, as it retains the diversity of sequences present in the biological sample from which it was prepared.
A xe2x80x9cpartially-fractionatedxe2x80x9d nucleic acid preparation may have undergone qualitative size-selection. In this case, uncleaved sequences, such as whole chromosomes or RNA molecules, are selectively retained or removed based upon size. In addition, a xe2x80x9cpartially-fractionatedxe2x80x9d preparation may comprise molecules that have undergone selection through hybridization to a sequence of interest; alternatively, a xe2x80x9cpartially-fractionatedxe2x80x9d preparation may have had undesirable sequences removed through hybridization. It is contemplated that a xe2x80x9cpartially-fractionatedxe2x80x9d pool of nucleic acid molecules will not comprise a single sequence that has been enriched after extraction from the biological sample to the point at which it is pure, or substantially pure.
In this context, xe2x80x9csubstantially purexe2x80x9d refers to a single nucleic acid sequence that is represented by a majority of nucleic acid molecules of the pool. Again, this refers to enrichment of a sequence in vitro; obviously, if a given sequence is heavily represented in the biological sample, a preparation containing it is not excluded from use according to the invention.
As used herein, the term xe2x80x9cbiological samplexe2x80x9d refers to a whole organism or a subset of its tissues, cells or component parts (e.g. fluids). xe2x80x9cBiological samplexe2x80x9d further refers to a homogenate, lysate or extract prepared from a whole organism or a subset of its tissues, cells or component parts, or a fraction or portion thereof. Lastly, xe2x80x9cbiological samplexe2x80x9d refers to a medium, such as a nutrient broth or gel in which an organism has been propagated, which contains cellular components, such as nucleic acid molecules.
As used herein, the term xe2x80x9corganismxe2x80x9d refers to all cellular life-forms, such as prokaryotes and eukaryotes, as well as non-cellular, nucleic acid-containing entities, such as bacteriophage and viruses.
As used herein, the term xe2x80x9cfeaturexe2x80x9d refers to each nucleic acid sequence occupying a discrete physical location on the array; if a given sequence is represented at more than one such site, each site is classified as a feature. In this context, the term xe2x80x9cnucleic acid sequencexe2x80x9d may refer either to a single nucleic acid molecule, whether double or single-stranded, to a xe2x80x9cclonexe2x80x9d of amplified copies of a nucleic acid molecule present at the same physical location on the array or to a replica, on a separate support, of such a clone.
As used herein, the term xe2x80x9camplifyingxe2x80x9d refers to production of copies of a nucleic acid molecule of the array via repeated rounds of primed enzymatic synthesis; xe2x80x9cin situ amplificationxe2x80x9d indicates that such amplifying takes place with the template nucleic acid molecule positioned on a support according to the invention, rather than in solution.
As used herein, the term xe2x80x9csupportxe2x80x9d refers to a matrix upon which nucleic acid molecules of a nucleic acid array are immobilized; preferably, a support is semi-solid.
As used herein, the term xe2x80x9csemi-solidxe2x80x9d refers to a compressible matrix with both a solid and a liquid component, wherein the liquid occupies pores, spaces or other interstices between the solid matrix elements.
As used herein in reference to the physical placement of nucleic acid molecules or features and/or their orientation relative to one another on an array of the invention, the terms xe2x80x9ccorrespondxe2x80x9d or xe2x80x9ccorrespondingxe2x80x9d refer to a molecule occupying a position on a second array that is either identical to- or a mirror image of the position of a molecule from which it was amplified on a first array which served as a template for the production of the second array, or vice versa, such that the arrangement of features of the array relative to one another is conserved between arrays of a plurality.
As implied by the above statement, a first and second array of a plurality of nucleic acid arrays according to the invention may be of either like or opposite chirality, that is, the patterning of the nucleic acid arrays may be either identical or mirror-imaged.
As used herein, the term xe2x80x9creplicaxe2x80x9d refers to any nucleic acid array that is produced by a printing process according to the invention using as a template a first randomly-patterned immobilized nucleic acid array.
As used herein, the term xe2x80x9cspotxe2x80x9d as applied to a component of a microarray refers to a discrete area of a surface containing a substance deposited by mechanical or other means.
As used herein, xe2x80x9cexcluded volumexe2x80x9d refers to the volume of space occupied by a particular molecule to the exclusion of other such molecules.
As used herein, xe2x80x9cexcess of nucleic acid moleculesxe2x80x9d refers to an amount of nucleic acid molecules greater than the amount of entities to which such nucleic acid molecules may bind. An excess may comprise as few as one molecule more than the number of binding entities, to twice the number of binding entities, up to 10 times, 100 times, 1000 times the number of binding entities or more.
As used herein, xe2x80x9csignal amplification methodxe2x80x9d refers to any method by which the detection of a nucleic acid is accomplished.
As used herein, a xe2x80x9cnucleic acid capture ligandxe2x80x9d or xe2x80x9cnucleic acid capture activityxe2x80x9d refers to any substance which binds nucleic acid molecules, either specifically or non-specifically, or which binds an affinity tag attached to a nucleic acid molecule in such a way as to immobilize the nucleic acid molecule to a support bearing the capture ligand.
As used herein, xe2x80x9creplica-destructivexe2x80x9d refers to methods of signal amplification which render an array or replica of an array non-reusable.
As used herein, the term xe2x80x9cnon-reusable,xe2x80x9d in reference to an array or replica of an array, indicates that, due to the nature of detection methods employed, the array cannot be replicated nor used for subsequent detection methods after the first detection method is performed.
As used herein, the term xe2x80x9cessentially distinctxe2x80x9d as applied to features of an array refers to the situation where 90% or more of the features of an array are not in contact with other features on the same array.
As used herein, the term xe2x80x9cpreservedxe2x80x9d as applied to the resolution of nucleic acid features on an array means that the features remain essentially distinct after a given process has been performed.
As used herein, the term xe2x80x9cdistinguishablexe2x80x9d as applied to a label, refers to a labeling moiety which can be detected when among other labeling moieties.
As used herein, the term xe2x80x9cspectrally distinguishablexe2x80x9d or xe2x80x9cspectrally resolvablexe2x80x9d as applied to a label, refers to a labeling moiety which can be detected by its characteristic fluorescent excitation or emission spectra, one or both of such spectra distinguishing said moiety from other moieties used separately or simultaneously in the particular method.
As used herein, the term xe2x80x9cchain-terminating analogxe2x80x9d refers to any nucleotide analog which, once incorporated onto the 3xe2x80x2 end of a nucleic acid molecule, cannot serve as a substrate for further addition of nucleotides to that nucleic acid molecule.
As used herein, the term xe2x80x9ctype IISxe2x80x9d refers to a restriction enzyme that cuts at a site remote from its recognition sequence. Such enzymes are known to cut at a distances from their recognition sites ranging from 0 to 20 base pairs.
It is preferred that the support is semi-solid.
Preferably, the semi-solid support is selected from the group that includes polyacrylamide, cellulose, polyamide (nylon) and cross-linked agarose, -dextran and -polyethylene glycol.
It is particularly preferred that amplifying of nucleic acid molecules of is performed by polymerase chain reaction (PCR).
Preferably, affixing of nucleic acid molecules to the support is performed using a covalent linker that is selected from the group that includes oxidized 3-methyl uridine, an acrylyl group and hexaethylene glycol. Additionally, Acrydite oligonucleotide primers may be covalently fixed within a polyacrylamide gel.
It is also contemplated that affixing of nucleic acid molecules to the support is performed via hybridization of the members of the pool to nucleic acid molecules that are covalently bound to the support.
As used herein, the term xe2x80x9csynthetic oligonucleotidexe2x80x9d refers to a short (10 to 1,000 nucleotides in length), double- or single-stranded nucleic acid molecule that is chemically synthesized or is the product of a biological system such as a product of primed or unprimed enzymatic synthesis.
As used herein, the term xe2x80x9ctemplate DNAxe2x80x9d refers to a plurality of DNA molecules used as the starting material or template for manufacture of a nucleic acid array such as a polyacrylamide-immobilized nucleic acid array.
As used herein, the term xe2x80x9ctemplate nucleic acidsxe2x80x9d refers to a plurality of nucleic acid molecules used as the starting material or template for manufacture of a nucleic acid array.
As used herein, the term xe2x80x9camplification primerxe2x80x9d refers to an oligonucleotide that may be used as a primer for amplification reactions. The term xe2x80x9cPCR primerxe2x80x9d refers to an oligonucleotide that may be used as a primer for the polymerase chain reaction. A PCR primer is preferably, but not necessarily, synthetic, and will generally be approximately 10 to 100 nucleotides in length.
As used herein, the term xe2x80x9cAcrydite modifiedxe2x80x9d in reference to an oligonucleotide means that the oligonucleotide has an Acrydite phosphoramidite group attached to the 5xe2x80x2 end of the molecule.
As used herein, the term xe2x80x9cthermostable, template-dependent DNA polymerasexe2x80x9d refers to an enzyme capable of conducting primed enzymatic synthesis following incubation at a temperature, greater than 65xc2x0 C. and less than or equal to approximately 100xc2x0 C., and for a time, ranging from about 15 seconds to about 5 minutes, that is sufficient to denature essentially all double stranded DNA molecules in a given population.
As used herein, the term xe2x80x9csolid supportxe2x80x9d refers to a support for a polyacrylamide-immobilized nucleic acid array, such support being essentially non-compressible and lacking pores containing liquid. A solid support is preferably thin and thermally conductive, such that changes in thermal energy characteristic of PCR thermal cycling are conducted through the support to permit amplification of PCR template molecules arrayed on its surface.
As used herein, the term xe2x80x9cbinding sitesxe2x80x9d when used in reference to a nucleic acid molecule, means sequences that hybridize under selected PCR annealing conditions with a selected PCR primer. Binding sites for PCR primers are generally used in pairs situated on either side of a sequence to be amplified, with each member of the pair preferably comprising a sequence from the other member of the pair.
As used herein, the term xe2x80x9cvariable sequencexe2x80x9d refers to a sequence in a population of nucleic acid molecules that varies between different members of the population. Generally, as used herein, a variable sequence is flanked on either side by sequences that are shared or constant among all members of that population.